Simple tools to detect the presence of genetically modified organisms (GMO) in commercial products represent a valuable aid in managing the legal requirements for GMO testing in a cost-effective way. The 'Real-Time PCR-Based Ready-to-Use Multi-Target Analytical System for GMO Detection' was developed to meet such requirements and was here further tested for its applicability on detecting GMO in recalcitrant matrices. Sixty-four highly processed maize products were purchased from the market of the European Union and analysed for their GMO content. Seventy-five percent of the test samples were positive for the presence of GMO. In one sample, trace amounts of a so-called asynchronously authorized GMO could be detected. The overall outcome of the analyses indicated that a good representation of the commercially available GMO for food use could be obtained by analysing a small subset of products. Finally, the use of the ‘Real-Time PCR-Based Ready-to-Use Multi-Target Analytical System for GMO Detection’ in detecting GMO reliably at the 0.1% mass level is documented. The implications of these results on the further development of such type of PCR-based GMO detection systems are discussed.